Use alembic instead of sqlalchemy-migrate; update to sqlalchemy 0.9

The motivations to move from sqlalchemy-migrate to alembic are described in the commit message and in #219.

The motivation to update to the current SQLAlchemy version is that it's actively developed, contains a lot of fixes, new features and some performance optimizations.

The SQLAlchemy update includes a fix for a backward incopability introduced in 0.8: the lack of mutable `PickleType` columns. This has been mitigated by a new class `MutableList`.

**Please don't merge yet:** As the upgrade to SQLAlchemy-0.9 includes the removal of sqlalchemy-migrate, remaining sqlalchemy-migrations have to be performed *before* this PR is merged. This will probably be done together with a release 2.0 due soon, together with upgrade hints.